README : BAMTOOLS
------------------------------------------------------------
-BamTools: a C++ API for reading/writing BAM files.
+BamTools: a C++ API & toolkit for reading/writing/manipulating BAM files.
I. Introduction
+ a. The API
+ b. The Toolkit
+
II. Usage
-III. Contact
+ a. The API
+ b. The Toolkit
+
+III. License
+
+IV. Acknowledgements
+
+V. Contact
------------------------------------------------------------
I. Introduction:
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
+
+
+Ia. The API:
+
The API consists of 2 main modules - BamReader and BamWriter. As you would expect,
-BamReader provides read-access to BAM files, while BamWriter does the writing of BAM
-files. BamReader provides an interface for random-access (jumping) in a BAM file,
+BamReader provides read-access to BAM files, while BamWriter handles writing data to
+BAM files. BamReader provides an interface for random-access (jumping) in a BAM file,
as well as generating BAM index files.
-An additional file, BamAux.h, is included as well.
-This file contains the common data structures and typedefs used throught the API.
+BamMultiReader is an extra module that allows you to manage multiple open BAM file
+for reading. It provides some validation & bookkeeping under the hood to keep all
+files sync'ed up for you.
+
+Additional files used by the API:
+ - BamAux.h : contains the common data structures and typedefs used throught the API.
+ - BamIndex.* : implements both the standard BAM format index (".bai") as well as a
+ new BamTools-specific index (".bti").
+ - BGZF.* : contains our implementation of the Broad Institute's BGZF compression format.
-BGZF.h & BGZF.cpp contain our implementation of the Broad Institute's
-BGZF compression format.
-BamConversion, BamDump, and BamTrim are 3 'toy' examples on how the API can be used.
+Ib. The Toolkit:
+
+If you've been using the BamTools since the early days, you'll notice that our 'toy' API
+examples (BamConversion, BamDump, BamTrim,...) are now gone. We dumped these in favor of
+a suite of small utilities that we hope both developers and end-users find useful:
+
+usage: bamtools [--help] COMMAND [ARGS]
+
+Available bamtools commands:
+ convert Converts between BAM and a number of other formats
+ count Prints number of alignments in BAM file(s)
+ coverage Prints coverage statistics from the input BAM file
+ filter Filters BAM file(s) by user-specified criteria
+ header Prints BAM header information
+ index Generates index for BAM file
+ merge Merge multiple BAM files into single file
+ random Select random alignments from existing BAM file(s)
+ sort Sorts the BAM file according to some criteria
+ stats Prints some basic statistics from input BAM file(s)
+
+See 'bamtools help COMMAND' for more information on a specific command.
+
+** Follow-up explanation here **
------------------------------------------------------------
II. Usage :
+** General usage information - perhaps explain common terms, point to SAM/BAM spec, etc **
+
+
+IIa. The API
+
To use this API, you simply need to do 3 things:
- 1 - Drop the BamTools files somewhere the compiler can find them.
- (i.e. in your source tree, or somewhere else in your include path)
+ 1 - Drop the BamTools API files somewhere the compiler can find them.
+ (i.e. in your project's source tree, or somewhere else in your include path)
2 - Import BamTools API with the following lines of code
- #include "BamReader.h" // as needed
+ #include "BamReader.h" // or "BamMultiReader.h", as needed
#include "BamWriter.h" // as needed
using namespace BamTools;
3 - Compile with '-lz' ('l' as in Lima) to access ZLIB compression library
- (For VS users, I can provide you zlib headers - just contact me).
+ (For MSVC users, I can provide you modified zlib headers - just contact me).
See any included programs and Makefile for more specific compiling/usage examples.
See comments in the header files for more detailed API documentation.
+
+IIb. The Toolkit
+
+** More indepth overview for the toolkit commands **
+
+------------------------------------------------------------
+
+III. License :
+
+Both the BamTools API and toolkit are released under the MIT License.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+See file LICENSE for details.
+
------------------------------------------------------------
-III. Contact :
+IV. Acknowledgements :
+
+ * Aaron Quinlan for several key feature ideas and bug fix contributions
+ * Baptiste Lepilleur for the public-domain JSON parser (JsonCPP)
+ * Heng Li, author of SAMtools - the original C-language BAM API/toolkit.
+
+------------------------------------------------------------
+
+V. Contact :
Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
- Derek Barnett
-
-http://sourceforge.net/projects/bamtools
+
+Marth Lab
+Biology Dept., Boston College
+
+Email: barnetde@bc.edu
+Project Websites: http://github.com/pezmaster31/bamtools (ACTIVE SUPPORT)
+ http://sourceforge.net/projects/bamtools (major updates only)
+
projects / bamtools.git / blobdiff